In a highly unusual confrontation, a Southern District judge and the U.S. Attorney’s Office in Manhattan are at loggerheads over the accuracy of a court transcript of the judge’s jury charge in a headline-grabbing criminal case involving leaders and lawyers of the New York City transit police union.

On April 8, Mark F. Pomerantz, chief of the U.S. Attorney’s Criminal Division, filed a sworn statement with the U.S. Court of Appeals for the Second Circuit asserting that Judge Deborah A. Batts’s chambers had amended the transcript of her charge in the Transit Patrolmen’s Benevolent Association case, putting it at odds with what she actually said when she delivered the charge on Jan. 22, 1998.